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RNAseq
Genome Assembly
Bioinformatics
1. Introduction
1.1 Introduction
1.2 The World of Mapping Programs
1.3 Why Do Biologists Need So Many Mapping Programs?
1.4 The Mapping Problem
1.5 Search Score and E-value
2. Core Algorithms
2.1 Smith-Waterman Algorithm
2.2 Increasing the Speed of Smith-Waterman
2.3 Indexing
2.4 Suffix Arrays
2.5 Reversible Transform and Data Compression
2.6 Burrows Wheeler Transform
2.7 Reversibility of BWT
2.7 LF Property
2.8 Reversibility of BWT
2.9 Thinking Conceptually about BWT
2.11 Search Using LF Property
2.12 FM Index
2.13 Summary
3. Advanced Concepts
3.1 Introduction
3.2 BWT-SW
3.3 Bidirectional BWT
3.4 SA-IS for Constructing Suffix Array
3.5 External Memory Construction of Suffix Array
3.6 Bauer-Cox-Rosone Algorithm for LightWeight BWT Construction
3.7 Lyndon Word and Lyndon Factorization
4. Implementations
4.1 The World of Mapping Programs
4.2 FASTA
4.3 BLAST
4.4 BLAT
4.5 Exonerate
4.6 Mummer
4.7 AVID
4.8 LAGAN
4.9 Mauve
4.11 Lastz
4.12 SSAHA
4.13 ELAND
4.14 SOAP
4.15 MAQ
4.16 SHRiMP
4.17 BWA
4.18 Bowtie
4.19 BFAST
4.21 Stampy
4.22 SOAP2
4.23 BWA-SW
4.24 Bowtie2
4.25 BLASR
4.26 BWA-MEM
4.27 Hidden Markov Model-based Algorithms
5. Hardware-accelerated Implementations
5.1 Introduction
5.2 Hardware-accelerated Smith-Waterman
5.3 GPU-accelerated SOAP3-dp
5.4 FPGA-accelerated Shepard
5.5 CPU-accelerated STAR
6. References and Future Challenges
6.1 Historical Developments on Suffix Array
6.2 Review Paper
6.3 Burrows Wheeler Transform
6.4 Mapping
6.5 Hardware Acceleration of Mapping
6.6 Unsolved problems
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SHRiMP
MAQ is another hash-based algorithm similar to ELAND and SOAP.